Evolution and origin of bread wheat

Functional characterization of TaWRKY254 in salt tolerance based on genome-wide analysis of the WRKY gene family in wheat core parent Zhou8425B

The WRKY gene family plays a pivotal role in regulating plant growth, development, and stress responses. Zhou8425B, a core wheat parent in Chinese breeding programs known for its superior agronomic traits, remains underexplored in terms of its WRKY functional landscape. In this study, we identified 294 WRKY transcription factors in the Zhou8425B genome and conducted comprehensive bioinformatics analyses covering gene structure, protein properties, phylogenetic relationships, conserved motifs, and cis-regulatory elements. RNA-seq analysis across 12 tissues revealed that 274 WRKY genes are highly expressed and form distinct tissue-specific clusters. Notably, TaWRKY254 (TraesZ8425B6B01G167200) was significantly upregulated under various environmental stresses. RT-qPCR confirmed that TaWRKY254 expression under salt stress was substantially higher in Zhou8425B compared to Chinese Spring. Sequence diversity analysis revealed a 513 bp deletion in the promoter region and a T-to-C nonsynonymous mutation in the exon, resulting in an isoleucine-to-valine substitution in Zhou8425B. Based on this 513 bp difference, we developed a specific molecular marker and genotyped the recombinant inbred lines (RILs) from a Zhou8425B × Chinese Spring. Phenotypic analysis showed that RILs carrying the TaWRKY254Zhou8425B genotype exhibited enhanced salt tolerance, as evidenced by increased catalase, proline, and soluble protein levels, reduced lipid peroxidation, and significantly higher thousand kernel weight compared to those with the TaWRKY254CS genotype. These findings suggest that TaWRKY254 may play an important role in salt stress adaptation and yield-related traits, highlighting its potential as a genetic resource for salt-tolerant wheat breeding.

Epigenetic perspectives on wheat speciation, adaptation, and development

Bread wheat (Triticum aestivum) has undergone a complex evolutionary history shaped by polyploidization, domestication, and adaptation. Recent advances in multiomics approaches have shed light on the role of epigenetic mechanisms, including DNA methylation, histone modification, chromatin accessibility, and noncoding RNAs, in regulating gene expression throughout these processes. Epigenomic reprogramming contributes to genome stability and subgenome differentiation and modulates key agronomic traits by influencing flowering time, environmental responses, and developmental programs. This review synthesizes current insights into epigenetic regulation of wheat speciation, adaptation, and development, highlighting their potential applications in crop improvement. A deeper understanding of these mechanisms will facilitate targeted breeding strategies leveraging epigenetic variations to enhance wheat resilience and productivity in the face of changing environments.

TaPP2C-a5 fine-tunes wheat seed dormancy and germination with a Triticeae-specific, alternatively spliced transcript

INTRODUCTION

The sessile plants often experience environmental conditions not ideal for growth, and therefore have evolved strategies to survive and adapt to stress conditions. Abscisic acid (ABA) regulates plant development and abiotic stress response. Clade A type 2C protein phosphatases (PP2Cs), act as co-receptors of ABA, negatively regulate ABA signalling. However, the biological function and detailed molecular mechanism of clade A PP2Cs in ABA signalling pathway remain to be elucidated in wheat.

OBJECTIVES

To analyze the mechanisms of stress response and development mediated by ABA signal precisely regulated by TaPP2C-a5 at the post-transcriptional level in wheat, providing candidate genes for wheat improvement.

METHODS

Based on our previous results of TaPP2Cs gene family analysis, the function and detailed regulation mechanisms of TaPP2C-a5 gene in seed dormancy and germination as well as drought response mediated by ABA signaling pathway were explored through reverse genetics technology.

RESULTS

We found that class A TaPP2C-a5 underwent alternative splicing (AS) to produce two transcripts encoding TaPP2C-a5.1 and TaPP2C-a5.2, respectively. Both TaPP2C-a5.1 and TaPP2C-a5.2 were highly expressed in mature seeds, and were upregulated by exogenous ABA in seedlings. Overexpression of TaPP2C-a5.1 and TaPP2C-a5.2 coordinately negatively regulated seed dormancy and ABA-mediated seed germination as well as post-germination developmental arrest in wheat. TaPP2C-a5.1 negatively regulated drought stress response, while TaPP2C-a5.2 did not participate in drought stress response. The homologous genes of TaPP2C-a5 underwent the same AS as TaPP2C-a5 in tetraploid wheat, but not in rice.

CONCLUSION

Our results revealed that TaPP2C-a5 gene underwent AS and was involved in the regulation of seed dormancy and germination, as well as drought stress response mediated by the ABA signaling at the post-transcriptional level. Our work not only provide a potential target gene to improve PHS resistance, but also emphasize alternative splicing as a strategy with evolution contexts to fine-tune ABA signaling and its involvement in certain biological process.

Genome-wide identification and characterization of NAC transcription factor-derived microsatellites in wheat (Triticum aestivum L.)

Bread wheat (Triticum aestivum L.) is one of the widely consumed staple foods, providing 20% of the total protein and calories in human nutrition. Seeing its importance in the global food supply, the enrichment of functional genomic resources is vital for meeting future demands and ensuring sustainable production. In addition to the presence of functional domains, the presence of microsatellites within transcription factors makes them valuable candidates for enriching functional marker resources. The NAC transcription factor family regulates a variety of physiological processes in cereal crops. Hence, the present study aims to develop and characterize Triticum aestivum NAC MicroSatellites (TaNACMS) to enrich functional marker resources for genetic diversity analysis, marker-assisted selection, and evolutionary studies. In total, 520 SSRs were identified from 451 TaNAC sequences, and a set of 66 TaNACMS was used for cross-transferability in wild/related wheat species. The cross-transferability rate of 90.22% revealed high locus conservation. Further, 16 TaNACMS were utilized for the characterization of genetic diversity in Indian wheat varieties. These TaNACMS produced 40 alleles (2.5 alleles per locus) with an average observed heterozygosity (Ho), expected heterozygosity (He), and polymorphic information content (PIC) of 0.392, 0.417, and 0.380, respectively. The genetic analysis of wheat genotypes, using principal coordinates analysis (PCoA), neighbor-joining (NJ) clustering, and Bayesian-based STRUCTURE, has revealed three distinct genetic clusters. Two of these clusters consist of Indian wheat varieties, while the third cluster comprises wild/related wheat species. In conclusion, the high rate of transferability of TaNACMS can be effectively utilized for gene flow both within and between species, highlighting evolutionary connections between cultivated wheat and related species. Additionally, these SSRs will aid the marker repository and benefit the wheat improvement programs through marker-assisted selection (MAS).

Genetic effect of the Ph1 locus on transcriptome atlas of anther development-related genes, meiotic chromosome behavior and agronomic traits in bread wheat

Proper spatiotemporal expression of meiosis-related genes (MRGs) and other male-microsporogenesis/microgametogenesis-related genes (MMRGs) is crucial for normal anther development, yet their expression patterns remain largely unknown in wheat. The Ph1 locus in wheat is known to contain the Ph1 gene that plays a dual role in promoting pairing between homologous chromosomes but repressing pairing between homoeologous chromosomes, but its genetic function is still unclear. Here, we investigated these issues by conducting a comprehensive transcriptome analysis during wheat anther development in Chinese Spring (CS) and its ph1b deletion mutant under greenhouse and field conditions. Our results revealed that MRGs and MMRGs are predominantly expressed during pre-meiosis stages, with MMRGs also being highly expressed in meiotic-II. Gene co-expression analysis showed that C2H2 and B3 transcriptional factors (TFs) are associated with MRGs, and MYB regulators interacted mainly with MMRGs during microgametogenesis. Deletion of genes within the Ph1 locus failed to induce compensatory transcriptional activation of their homoeologous counterparts, while genes outside the Ph1 locus showed environmental-specific responses, especially during meiotic-II and mature pollen stages. Notably, early disjunction of bivalent chromosomes is a primary factor leading to defective meiocytes during metaphase I. Furthermore, the ph1b deletion mutant exhibited a substantially delayed heading date, potentially contributing to environment-stable and environment-specific alterations in fertility and grain-related traits. Our study highlights the significant impact of the Ph1 locus on the transcriptome during anther development, and a previously unheeded effect on meiotic chromosome pairing and agronomic traits, suggesting potential for genetic manipulations within the Ph1 locus for wheat improvement.

Wheat Histone Deacetylase TaZIHD1 Interacts with Transcriptional Repressor TaZPAW1 to Negatively Regulate Zinc Uptake

Zinc (Zn) is a chemical element essential to plant growth and development, and soil Zn deficiency restricts agricultural production. Understanding the regulatory mechanism of Zn uptake in bread wheat (Triticum aestivum) is critical for improving wheat production in Zn-deficient regions. In this study, wheat zinc-regulated transporters, iron-regulated transporter-like protein 10 (TaZIP10) was identified as a functional Zn transporter. The TaZIP10 protein exhibits Zn-transport activity in yeast and localizes to the plant plasma membrane. The TaZIP10 gene is mainly expressed in wheat roots, and its expression is induced by Zn deficiency. Silencing of the TaZIP10 gene resulted in the decreased Zn acquisition in wheat seedlings. Furthermore, we demonstrated that the TaZIP10 promoter-associated WRKY-type transcription factor 1 (TaZPAW1) directly binds to TaZIP10 promoter regions and functions as a transcriptional repressor. Importantly, we found that TaZPAW1 interacts with the histone deacetylase TaZIHD1 (TaZPAW1-interacting histone deacetylase 1) and recruits TaZIHD1 to the TaZIP10 promoter regions to mediate histone deacetylation, which leads to the epigenetic suppression of TaZIP10 expression. In addition, we showed that silencing of the wheat TaZPAW1 or TaZIHD1 gene resulted in the potentiated Zn acquisition. These findings support that the wheat WRKY-type transcription factor functions in concert with histone deacetylase to negatively regulate Zn uptake presumably via epigenetically suppressing the Zn transporter gene.

Transcription factors in Orinus: novel insights into transcription regulation for speciation adaptation on the Qinghai-Xizang (Tibet) Plateau

BACKGROUND

Transcription factors (TFs) are crucial regulators of plant growth, development, and resistance to environmental stresses. However, comprehensive understanding of the roles of TFs in speciation of Orinus, an extreme-habitat plant on the Qinghai-Xizang (Tibet) Plateau, is limited.

RESULTS

Here, we identified 52 TF families, including 2125 members in Orinus, by methodically analysing domain findings, gene structures, chromosome locations, conserved motifs, and phylogenetic relationships. Phylogenetic trees were produced for each Orinus TF family using protein sequences together with wheat (Triticum aestivum L.) TFs to indicate the subgroups. The differences between Orinus and wheat species in terms of TF family size implies that both Orinus- and wheat-specific subfamily contractions (and expansions) contributed to the high adaptability of Orinus. Based on deep mining of RNA-Seq data between two species of Orinus, O. thoroldii and O. kokonoricus, we obtained differentially expressed TFs (DETFs) in 20 families, most of which were expressed higher in O. thoroldii than in O. kokonoricus. In addition, Cis-element analysis shows that MYC and G-box elements are enriched in the promoter region of DETFs, suggesting that jasmonic acid (JA) and abscisic acid (ABA) act synergistically in Orinus to enhance the signalling of related abiotic stress responses, ultimately leading to an improvement in the stress tolerance and speciation adaptation of Orinus.

CONCLUSIONS

Our data serve as a genetic resource for Orinus, not only filling the gap in studies of TF families within this genus but also providing preliminary insights into the molecular mechanisms underlying speciation in Orinus.

Bioinformatics analysis and development of functional markers for TaMYB4-1A in wheat

MYB transcription factors play crucial roles in various stages of plant growth and development. Bioinformatics analysis revealed that wheat TaMYB4-1A contains two conserved MYB domain. The coding region of TaMYB4-1A is 792 bp, encoding 263 amino acids. TaMYB4-1A is a hydrophilic protein, and its encoded protein is localized in the cell nucleus. Evolutionary tree analysis indicates that the TaMYB4 protein shares the closest relationship with Aegilops, barley, and rye. Tissue-specific expression analysis revealed that TaMYB4-1A is expressed in wheat roots, stems, leaves, and seeds 14 days post-flowering, with the highest expression in the seeds. Promoter cis-acting element analysis showed that the promoter region of TaMYB4-1A contains various cis-acting elements, including meristem regulatory elements, drought-induced elements, and hormone response elements. qRT-PCR analysis showed that the expression of TaMYB4-1A is suppressed under high salinity and PEG treatment, suggesting that TaMYB4-1A may play a critical regulatory role in response to salt and drought stress. There are two haplotypes of TaMYB4-1A, namely Hap-1A-I and Hap-1A-II. The average plant height of varieties with haplotype Hap-1A-I is significantly higher than that of varieties with haplotype Hap-1A-II. This research provides a basis for future in-depth investigation of the biological function of the TaMYB4-1A gene and offers promising candidate genes for molecular marker-assisted wheat breeding.

Selection of dysfunctional alleles of bHLH1 and MYB1 has produced white grain in the tribe Triticeae

Grain color is a key agronomic trait that greatly determines food quality. The molecular and evolutionary mechanisms that underlie grain-color regulation are also important questions in evolutionary biology and crop breeding. Here, we confirm that both bHLH and MYB genes have played a critical role in the evolution of grain color in Triticeae. Blue grain is the ancestral trait in Triticeae, whereas white grain caused by bHLH or MYB dysfunctions is the derived trait. HvbHLH1 and HvMYB1 have been the targets of selection in barley, and dysfunctions caused by deletion(s), insertion(s), and/or point mutation(s) in the vast majority of Triticeae species are accompanied by a change from blue grain to white grain. Wheat with white grains exhibits high seed vigor under stress. Artificial co-expression of ThbHLH1 and ThMYB1 in the wheat endosperm or aleurone layer can generate purple grains with health benefits and blue grains for use in a new hybrid breeding technology, respectively. Our study thus reveals that white grain may be a favorable derived trait retained through natural or artificial selection in Triticeae and that the ancient blue-grain trait could be regained and reused in molecular breeding of modern wheat.

Horizontally acquired CSP genes contribute to wheat adaptation and improvement

Although horizontal gene transfer (HGT) often facilitates environmental adaptation of recipient organisms, whether and how they might affect crop evolution and domestication is unclear. Here we show that three genes encoding cold-shock proteins (CSPs) were transferred from bacteria to Triticeae, a tribe of the grass family that includes several major staple crops such as wheat, barley and rye. The acquired CSP genes in wheat (TaCSPs) are functionally conserved in their bacterial homologues by encoding a nucleic acid-binding protein. Experimental evidence indicates that TaCSP genes positively regulate drought response and improve photosynthetic efficiency under water-deficient conditions by directly targeting a type 1 metallothionein gene to increase reactive oxygen species scavenging, which in turn contributed to the geographic expansion of wheat. We identified an elite CSP haplotype in Aegilops tauschii, introduction of which to wheat significantly increased drought tolerance, photosynthetic efficiency and grain yields. These findings not only provide major insights into the role of HGT in crop adaptation and domestication, but also demonstrate that novel microbial genes introduced through HGT offer a stable and naturally optimized resource for transgenic crop breeding and improvement.

A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat

The complete assembly of vast and complex plant genomes, like the hexaploid wheat genome, remains challenging. Here we present CS-IAAS, a comprehensive telomere-to-telomere (T2T) gap-free Triticum aestivum L. genome, encompassing 14.51 billion base pairs and featuring all 21 centromeres and 42 telomeres. Annotation revealed 90.8 Mb additional centromeric satellite arrays and 5,611 rDNA units. Genome-wide rearrangements, centromeric elements, transposable element expansion and segmental duplications were deciphered during tetraploidization and hexaploidization, providing a comprehensive understanding of wheat subgenome evolution. Among them, transposable element insertions during hexaploidization greatly influenced gene expression balances, thus increasing the genome plasticity of transcriptional levels. Additionally, we generated 163,329 full-length cDNA sequences and proteomic data that helped annotate 141,035 high-confidence protein-coding genes. The complete T2T reference genome (CS-IAAS), along with its transcriptome and proteome, represents a significant step in our understanding of wheat genome complexity and provides insights for future wheat research and breeding.

Integrated review of Psathyrostachy huashanica: From phylogenetic research to wheat breeding application

Enhancing wheat yield and stress tolerance is a critical long-term objective for global food security. Historically, breeders selected genetic traits from wild wheat relatives for domesticated targets, such as non-shattering and free threshing characteristics, and developed the cultivated wheat. However, the genetic diversity of the cultivated wheat has become narrow after long-term domestication and conscious selection, which seriously limited the yield potential and stress tolerance. Therefore, using wild Triticeae species to broaden the gene pool is an ongoing task for wheat improvement. Psathyrostachy huashanica Keng ex P. C. Kuo (2n = 2x = 14, NsNs), a perennial species of the genus Psathyrostachys Nevski, is restrictively distributed in the Huashan Mountain region of Shaanxi province, China. P. huashanica exhibits considerable potential for wheat breeding due to its valuable agronomic traits such as early maturation, more tillers, abiotic tolerance, and biotic resistance. Over the past four decades, researchers have successfully crossed P. huashanica with common wheat and developed derivative lines with improved agronomic traits. Here, we summarized the morphology, genomic evolution, and derived wheat breeding lines with advanced agronomic characteristics inherited from P. huashanica. This review provides a useful guideline for future research on P. huashanica, and highlights its importance in wheat breeding.

Wheat Chromatin Remodeling Protein TaSWP73 Contributes to Compatible Wheat-Powdery Mildew Interaction

Wheat powdery mildew disease caused by the obligate biotrophic fungal pathogen Blumeria graminis forma specialis tritici (B.g. tritici) seriously threatens global wheat production. Although improved powdery mildew resistance is an aim in wheat breeding, the regulatory mechanism underlying the wheat-B.g. tritici interaction remains poorly understood. In this study, the wheat chromatin remodeling protein TaSWP73 was identified as a negative regulator of post-penetration resistance against B.g. tritici. The transient overexpression of TaSWP73 attenuates wheat post-penetration resistance against B.g. tritici, while the silencing of TaSWP73 potentiates salicylic acid (SA) biosynthesis and activates post-penetration resistance against B.g. tritici. Importantly, chromatin in the promoter regions of TaSARD1, an activator gene of SA biosynthesis, is marked by high nucleosome occupancy in the TaSWP73-silenced wheat leaves. The silencing of TaSARD1 could suppress SA biosynthesis and attenuate post-penetration resistance against B.g. tritici with a lack of TaSWP73. In addition, TaICS1 was characterized as an essential component of wheat SA biosynthetic machinery. Potentiated SA biosynthesis and increased post-penetration resistance against B.g. tritici with a lack of TaSWP73 could be suppressed by the silencing of TaICS1 expression. These results collectively support the hypothesis that the wheat chromatin remodeling protein TaSWP73 contributes to the compatible wheat-powdery mildew interaction presumably via the suppression of the TaSARD1-TaICS1-SA pathway.

Advances in Mechanisms of Anaphylaxis in Wheat Allergy: Utility of Rodent Models

Wheat is a staple and nutritious food that is consumed globally. However, it is identified as a major allergenic food because of its capacity to trigger life-threatening systemic anaphylaxis. The specific mechanisms that underlie this systemic anaphylaxis in wheat allergy are incompletely understood. As a result, several rodent models have been developed to study anaphylaxis in wheat allergies. In this paper, we have conducted a comprehensive review of wheat-induced anaphylaxis using Google Scholar and PubMed databases with relevant keywords. The following objectives were addressed: (1) to determine the complexity of wheat-induced anaphylaxis; (2) to summarize the role of genetic susceptibility in wheat anaphylaxis; (3) to identify the environmental factors involved in the development of wheat anaphylaxis; (4) to map the current status of mechanisms involved in wheat anaphylaxis; (5) to identify the approaches, strengths, and limitations of rodent models of wheat anaphylaxis; and (6) to identify challenges and opportunities in this area of science. Our findings provide a comprehensive updated critical resource for the future research agenda in wheat allergy-associated anaphylaxis, particularly using rodent models as attractive pre-clinical tools.

Fossil or Non-Fossil: A Case Study in the Archaeological Wheat Triticum parvicoccum (Poaceae: Triticeae)

BACKGROUND/OBJECTIVES

The archaeobotanical taxon "Triticum parvicoccum" was first described in 1980 as a small-grained, naked, free-threshing, and dense ear tetraploid wheat species (2n = 4x = 28) identified from archaeological remains. This primitive tetraploid, cultivated in the Levant approximately 9000 years ago and subsequently dispersed throughout the Fertile Crescent, represents a potential contributor of the BBAA genomes to T. aestivum. This study aims to resolve the complex nomenclatural status of this taxon, which has remained ambiguous due to competing interpretations under fossil and non-fossil taxonomic regulations.

METHODS

We conducted a comprehensive nomenclatural review to evaluate the taxonomic validity of T. parvicoccum, analyzing previous research on the classification of archaeobotanical materials in relation to fossil status.

RESULTS

Our analysis demonstrated that archaeobotanical materials do not qualify as fossils and led to the validation of the taxon at a subspecific rank as a non-fossil entity: T. turgidum subsp. parvicoccum Kislev. subsp. nov. The holotype was established using a charred rachis fragment from Timnah (Tel Batash), an archaeological site on the inner Coastal Plain (Shfela) adjacent to the western piedmont of the Judean Mountains, Israel.

CONCLUSIONS

This study resolves the longstanding nomenclatural uncertainty surrounding this archaeologically significant wheat taxon, providing a valid taxonomic designation that reflects its biological and historical importance while adhering to current botanical nomenclature standards.

Genome-Wide Identification of the CIF Gene Family and Protein Interaction with GSO1s Under the p-HBA-Induced Continuous Cropping Obstacle in Pogostemon cablin

Casparian strip integrity factors (CIFs), which are tyrosine-sulfated small peptides, are crucial genes involved in the formation and regulation of the Casparian strip and play an important role in the regulation of plant stress response. In order to explore the evolution, characteristics, role, and function of CIFs in response to continuous cropping obstacles (CCOs), the bioinformatics and gene expression analysis of CIF genes in Pogostemon cablin was carried out by determining the phylogenetic relationship, chromosome location, gene structure, and RT-qPCR results. Results showed that a total of 12 PatCIF family genes were identified on 12 different chromosomes. Promoter prediction analysis revealed 16 different cis-regulatory elements. A systematic evolutionary study of 33 species indicates CIF family genes originated from Spermatophyta. Collinearity analysis revealed P. cablin shared 19 syntenic genes with Solanum lycopersicum and only 8 with Oryza sativa. Transcriptome analysis indicated that the expression of PatCIF1-4 and PatGSO1b/1c/1f genes decreased under p-hydroxybenzoic acid treatment, and further RT-qPCR validation of four PatCIF genes was consistent with the results. AlphaFold prediction showed a protein interaction region between PatCIF1-4 mature peptide and PatGSO1b/1c/1f via the LRR domain, which provides a key binding surface for mature PatCIFs. This study offers a theoretical basis to investigate the roles of PatCIFs and PatGSO1s in CCOs and their protein interactions in P. cablin.

Genome-wide identification and expression analysis of phytochrome gene family in Aikang58 wheat (Triticum aestivum L.)

Phytochromes are essential photoreceptors in plants that sense red and far-red light, playing a vital role in regulating plant growth and development through light signal transduction. Despite extensive research on phytochromes in model plants like Arabidopsis and rice, they have received relatively little attention in wheat. In this study, we employed bioinformatics methods to identify eight TaAkPHY genes in the Aikang58 wheat variety. Based on gene structure, conserved domains, and phylogenetic relationships, the TaAkPHY gene family exhibits a high degree of conservation. Synteny analysis revealed the evolutionary history of the PHY genes in Aikang58 and Chinese Spring wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rice (Oryza sativa L.), maize (Zea mays L.), quinoa (Chenopodium quinoa Willd.), soybean [Glycine max (L.) Merr.], and Arabidopsis [Arabidopsis thaliana (L.) Heynh.]. Among these species, wheat is most closely related to barley, followed by rice and maize. The cis-acting element analysis indicates that the promoter regions of TaAkPHY genes contain a large number of CAT-box, CGTCA-motif, GC-motif, etc., which are mainly involved in plant development, hormone response, and stress response. Gene expression profiling demonstrated that TaAkPHY genes exhibit varying expression levels across different tissues and are induced by various stress conditions and plant hormone treatments. Co-expression network analysis suggested that TaAkPHY genes may specifically regulate downstream genes associated with stress responses, chloroplast development, and circadian rhythms. Additionally, the least absolute shrinkage and selection operator (LASSO) regression algorithm in machine learning was used to screen transcription factors such as bHLH, WRKY, and MYB that influenced the expression of TaAkPHY genes. This method helps to quickly extract key influencing factors from a large amount of complex data. Overall, these findings provide new insights into the role of phytochromes in wheat growth, development, and stress responses, laying a foundation for future research on phytochromes in wheat.

Unraveling Effects of miRNAs Associated with APR Leaf Rust Resistance Genes in Hybrid Forms of Common Wheat (Triticum aestivum L.)

The fungus Puccinia triticina Eriks (Pt) is the cause of leaf rust, one of the most damaging diseases, which significantly reduces common wheat yields. In Pt-resistant adult plants, an APR-type resistance is observed, which protects the plant against multiple pathogen races and is distinguished by its persistence under production conditions. With a more complete understanding of the molecular mechanisms underlying the function of APR genes, it will be possible to develop new strategies for resistance breeding in wheat. Currently, mainly APR genes, such as Lr34, Lr46, and Lr67, are principally involved in resistance breeding as they confer durable resistance to multiple fungal races occurring under different climatic and environmental conditions. However, the mechanisms underlying the defence against pathogens mediated by APR genes remain largely unknown. Our research aimed to shed light on the molecular mechanisms related to resistance genes and miRNAs expression, underlying APR resistance to leaf rust caused by Pt. Furthermore, the present study aimed to identify and functionally characterize the investigated miRNAs and their target genes in wheat in response to leaf rust inoculation. The plant material included hybrid forms of wheat from the F2 and BC1F1 generations, obtained by crossing the resistance cultivar Glenlea (CItr 17272) with agriculturally important Polish wheat cultivars. Biotic stress was induced in adult plants via inoculation with Pt fungal spores under controlled conditions. The RT-qPCR method was used to analyze the expression profiles of selected APR genes at five time points (0, 6, 12, 24, and 48 hpi). The results presented here demonstrate the differential expression of APR genes and miRNAs at stages of leaf rust development at selected timepoints after inoculation. We analyzed the expression of three leaf rust resistance genes, using different genetic backgrounds in F2 and BC1F1 segregation materials, in leaf tissues after Pt infection. Our goal was to investigate potential differences resulting from the genetic background found in different generations of hybrid forms of the same parental forms. Gene ontology analysis predicted 190 target genes for tae-miR5384-3p and 167 target genes for tae-miR9653b. Our findings revealed distinct expression profiles for genes, with the highest expression levels observed mainly at 6, 24, and 48 hpi. The candidate gene Lr46-Glu2 displayed an upregulation, suggesting its potential involvement in the immune response against Pt infection.

Dissection of QTLs underlying the genetic basis of drought resistance in wheat: a meta-analysis

Wheat (Triticum aestivum L.) is one of the most important cereal crops, with its grain serving as a predominant staple food source on a global scale. However, there are many biotic and abiotic stresses challenging the stability of wheat production. Among the abiotic stresses, drought is recognized as a significant stress and poses a substantial threat to food production and quality throughout the world. Raising drought tolerance of wheat varieties through genetic regulation is therefore considered as one of the most effective ways to combat the challenges caused by drought stress. Meta-QTL analysis has demonstrated its effectiveness in identifying consensus QTL regions in wheat drought resistance in numerous instances. In this study, we present a comprehensive meta-analysis aimed at unraveling the drought tolerance genetic basis associated with agronomic traits in bread wheat. Extracting data from 34 previously published studies, we aggregated a corpus of 1291 Quantitative Trait Loci (QTL) pertinent to wheat drought tolerance. Then, the translation of the consensus genetic map yielded a comprehensive compendium of 49 distinct MQTLs, each associated with diverse agronomic traits. Prominently featured among the MQTLs were MQTLs 1.1, 1.7, 1.8 (1D), 4.1 (4A), 4.6 (4D), 5.2 (5B), 6.6 (6B), and 7.2 (7B), distinguished as pivotal MQTLs offering significant potential for application in marker-assisted breeding endeavors. Altogether, a total of 66 putative candidate genes (CGs)-related drought tolerance were identified. This work illustrates a translational research approach in transferring information from published mapping studies to genomic regions hosting major QTLs governing key agronomical traits in wheat.

Comparative analysis of Aegilops speltoides and wheat repetitive elements and development of S genome-specific FISH painting

Aegilops speltoides (2n = 2x = 14, genome SS) is a wild relative of wheat and a donor of useful traits for wheat improvement. Several whole-genome studies compared genic regions of Aegilops from the Sitopsis section and wheat and found that Ae. speltoides is most closely related to the wheat B subgenome but is not its direct progenitor. The results showed that a B subgenome ancestor diverged from Ae. speltoides more than 4 MYA and either has not yet been discovered, or is extinct. To further explore the evolutionary relationship between wheat and Ae. speltoides and develop Ae. speltoides chromosome paints, we performed comparative analysis of repetitive fractions of the S genome and three subgenomes of hexaploid wheat. The low-coverage sequence data were analyzed with RepeatExplorer pipeline to annotate repeats and estimate their content. The LTR-retrotransposons comprised about 80% of repeats in Ae. speltoides and wheat datasets and about two-third of them were LTR/Ty3-Gypsy. Ae. speltoides had 1.5 times more LTR/Ty-Copia repeats and 1.5 times less DNA transposons than wheat subgenomes. Several S genome-specific dispersed repeats were found and annotated. Their sequences were used to develop S genome-specific paints for detecting Ae. speltoides chromatin in the wheat background using fluorescent in situ hybridization.

The highly dynamic satellitomes of cultivated wheat species

BACKGROUND AND AIMS

Durum wheat, Triticum turgidum, and bread wheat, Triticum aestivum, are two allopolyploid species of very recent origin that have been subjected to intense selection programmes during the thousands of years they have been cultivated. In this paper, we study the durum wheat satellitome and establish a comparative analysis with the previously published bread wheat satellitome.

METHODS

We revealed the durum wheat satellitome using the satMiner protocol, which is based on consecutive rounds of clustering of Illumina reads by RepeatExplorer2, and we estimated abundance and variation for each identified satellite DNA (satDNA) with RepeatMasker v4.0.5. We also performed a deep satDNA family characterization including chromosomal location by fluorescence in situ hybridization (FISH) in durum wheat and its comparison with FISH patterns in bread wheat. BLAST was used for trailing each satDNA in the assembly of durum wheat genome through NCBI's Genome Data Viewer and the genome assemblies of both species were compared. Sequence divergence and consensus turnover rate between homologous satDNA families of durum and bread wheat were estimated using MEGA11.

KEY RESULTS

This study reveals that in an exceedingly short period, significant qualitative and quantitative changes have occurred in the set of satDNAs of both species, with expansions/contractions of the number of repeats and the loci per satellite, different in each species, and a high rate of sequence change for most of these satellites, in addition to the emergence/loss of satDNAs not shared between the two species analysed. These evolutionary changes in satDNA are common between species but what is truly remarkable and novel is that these processes have taken place in less than the last ~8000 years separating the two species, indicating an accelerated evolution of their satDNAs.

CONCLUSIONS

These results, together with the relationship of many of these satellites with transposable elements and the polymorphisms they generate at the level of centromeres and subtelomeric regions of their chromosomes, are analysed and discussed in the context of the evolutionary origin of these species and the selection pressure exerted by humans throughout the history of their cultivation.

Genome-Wide Identification and Expression Analysis of NF-YA Gene Family in the Filling Stage of Wheat (Triticum aestivum L.)

The NF-YA gene family is a highly conserved transcription factor that plays a crucial role in regulating plant growth, development, and responses to various stresses. Despite extensive studies in multiple plants, there has been a dearth of focused and systematic analysis on NF-YA genes in wheat grains. In this study, we carried out a comprehensive bioinformatics analysis of the NF-YA gene family in wheat, using the latest genomic data from the Chinese Spring. A total of 19 TaNF-YA genes were identified. An analysis of conserved domains, phylogenetic relationships, and gene structure indicated a significant degree of conservation among TaNF-YAs. A gene collinearity analysis demonstrated that fragment duplication was the predominant mechanism driving the amplification of TaNF-YAs. Furthermore, cis-acting elements within the promoters of TaNF-YAs were found to be implicated in grain development. Subsequently, SNP analysis revealed the genetic variation in the NF-YA gene family in different wheat. Moreover, published RNA-seq data were used and RNA-seqs of Pinyu8155, Yaomai30, Yaomai36, and Pinyu8175 were performed to identify TaNF-YAs influencing grain development. Finally, it was found that NF-YAs had no self-activating activity in wheat. This study provides key candidate genes for the exploration of grain development in the wheat filling stage and also lays a foundation for further research on the regulation of starch and protein synthesis and accumulation.

Cytological mapping of a powdery mildew resistance locus PmRc1 based on wheat-Roegneria ciliaris structural rearrangement library

KEY MESSAGE

A powdery mildew (Pm) resistance locus PmRc1 was identified and transferred from Roegneria ciliaris into wheat. Two compensative translocation lines carrying PmRc1 were developed. Powdery mildew (Pm), caused by the biotrophic fungal pathogen Blumeria graminis f.sp. tritici (Bgt), is a global destructive disease of bread wheat (Triticum aestivum L.). Identifying and utilizing new Pm resistance gene(s) is the most fundamental work for disease control. Roegneria ciliaris (2n = 4 x= 28, genome ScScYcYc) is a wild relative species of cultivated wheat. In this work, we evaluated wheat-R. ciliaris disomic chromosome addition lines for Pm resistance in multiple years. The introduction of R. ciliaris chromosome 1Sc into wheat enhanced resistance. The resistance locus on 1Sc was designated as PmRc1. To cytologically map PmRc1, we induced structural rearrangements using ion irradiation and increasing homoeologous chromosomal recombination. The identified 43 1Sc translocation or deletion lines were used to construct 1Sc cytological bin map by marker analysis using 111 molecular markers. Based on the Pm resistance of the characterized structural rearrangement lines, the PmRc1 locus was cytologically mapped to bin 1ScS-8 of 1Sc short arm, flanked by markers CMH93-2 and CMH114-1. Two compensatory chromosomal translocation lines (T1ScS · 1BL and T1ScS-1AS · 1AL) carrying PmRc1 were developed and assessed for their agronomic traits. Translocation chromosome T1ScS · 1BL had enhanced Pm resistance accompanied by negative effects on grain number and single plant yield. Translocation chromosome T1ScS-1AS · 1AL had enhanced Pm resistance and increased spikelet number per spike, without any obvious negative effect on other tested traits. Thus, T1ScS-1AS · 1AL is recommended preferentially used in wheat breeding for Pm resistance.

Development of an HPPD-Inhibitor Resistant Wheat and Multiomics Integrative Analysis of Herbicide Toxicity and OsHIS1 Detoxification in Wheat

Weed infestation in agricultural fields significantly diminishes crop yields. Herbicides are widely used as a primary method of weed control. Developing herbicide-resistant crops through the expression of resistant genes represents a sustainable approach. This study generated wheat germplasms highly resistant to 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibiting herbicides by transforming the rice HPPD INHIBITOR SENSITIVE 1 (OsHIS1) gene into Xinong 511, conferring resistance to mesotrione at levels up to nine times the typical field application rate (1350 g ai ha-1). Agronomic trait evaluations under greenhouse and field conditions showed no additional effects on wheat. Herbicide susceptibility assays confirmed the specific resistance to different HPPD inhibitors. Transcriptome and metabolome analyses revealed regulation of flavonoid and photosynthesis-antenna protein pathways in the herbicide functional. Collectively, OsHIS1 could be applied in the production of herbicide-resistant wheat.

Unveiling RNA structure-mediated regulations of RNA stability in wheat

Despite the critical role of mRNA stability in post-transcriptional gene regulation, research on this topic in wheat, a vital agricultural crop, remains unclear. Our study investigated the mRNA decay landscape of durum wheat (Triticum turgidum L. ssp. durum, BBAA), revealing subgenomic asymmetry in mRNA stability and its impact on steady-state mRNA abundance. Our findings indicate that the 3' UTR structure and homoeolog preference for RNA structural motifs can influence mRNA stability, leading to subgenomic RNA decay imbalance. Furthermore, single-nucleotide variations (SNVs) selected for RNA structural motifs during domestication can cause variations in subgenomic mRNA stability and subsequent changes in steady-state expression levels. Our research on the transcriptome stability of polyploid wheat highlights the regulatory role of non-coding region structures in mRNA stability, and how domestication shaped RNA structure, altering subgenomic mRNA stability. These results illustrate the importance of RNA structure-mediated post-transcriptional gene regulation in wheat and pave the way for its potential use in crop improvement.

On the evolution and genetic diversity of the bread wheat D genome

Bread wheat (Triticum aestivum) became a globally dominant crop after incorporating the D genome from the donor species Aegilops tauschii, but the evolutionary history that shaped the D genome during this process remains to be clarified. Here, we propose a renewed evolutionary model linking Ae. tauschii and the hexaploid wheat D genome by constructing an ancestral haplotype map covering 762 Ae. tauschii and hexaploid wheat accessions. We dissected the evolutionary trajectories of Ae. tauschii lineages and reported a few independent intermediate accessions, demonstrating that low-frequency inter-sublineage gene flow had enriched the diversity of Ae. tauschii. We discovered that the D genome of hexaploid wheat was inherited from a unified ancestral template, but with a mosaic composition that was highly mixed and derived mainly from three Ae. tauschii L2 sublineages located in the Caspian coastal region. This result suggests that early agricultural activities facilitated innovations in D-genome composition and finalized the success of hexaploidization. We found that the majority (51.4%) of genetic diversity was attributed to novel mutations absent in Ae. tauschii, and we identified large Ae. tauschii introgressions from various lineages, which expanded the diversity of the wheat D genome and introduced beneficial alleles. This work sheds light on the process of wheat hexaploidization and highlights the evolutionary significance of the multi-layered genetic diversity of the bread wheat D genome.

Decrease in purifying selection pressures on wheat homoeologous genes: tetraploidization versus hexaploidization

A series of polyploidizations in higher-order polyploids is the main event affecting gene content in a genome. Each polyploidization event can lead to massive functional divergence because of the subsequent decrease in selection pressure on duplicated genes; however, the causal relationship between multiple rounds of polyploidization and the functional divergence of duplicated genes is poorly understood. We focused on the Triticum-Aegilops complex lineage and compared selection pressure before and after tetraploidization and hexaploidization events. Although both events led to decreased selection pressure on homoeologous gene pairs (compared with diploids and tetraploids), the initial tetraploidization had a greater impact on selection pressure on homoeologous gene pairs than did subsequent hexaploidization. Consistent with this, selection pressure on expression patterns for the initial event relaxed more than those for the subsequent event. Surprisingly, the decreased selection pressure on these homoeologous genes was independent of the existence of in-paralogs within the same subgenome. Wheat homoeologous pairs had different evolutionary consequences compared with orthologs related to other mechanisms (ancient allopolyploidization, ancient autopolyploidization, and small-scale duplication). Furthermore, tetraploidization and hexaploidization also seemed to have different evolutionary consequences. This suggests that homoeologous genes retain unique functions, including functions that are unlikely to be preserved in genes generated by the other duplication mechanisms. We found that their unique functions differed between tetraploidization and hexaploidization (e.g., reproductive and chromosome segregation processes). These findings imply that the substantial number of gene pairs resulting from multiple allopolyploidization events, especially initial tetraploidization, may have been a unique source of functional divergence.

A highly potential Zn biofortification tool: MTP1 in Triticum aestivum

TaMTPs belong to metal tolerance proteins (MTPs) family in common wheat and have significant potential to address the "hidden hunger" caused by inadequate dietary intake of a key micronutrient (Zn). In this study, a total of 33 MTP members in Triticum aestivum were identified, among which six TaMTP1-likes were closely related to Arabidopsis thaliana MTP1 and were designated as TaMTP1-A/B/D and TaMTP1.1-A/B/D. When heterologously expressed in yeast mutants, TaMTP1-likes complemented their hypersensitivity to Zn and Co, and three of the most metal-resistant members, TaMTP1-A, TaMTP1-D and TaMTP1.1-B, were selected for further subcellular localization and functional experiment in Arabidopsis and rice. The results showed that all three proteins were localized in the vacuole membrane, that TaMTP1-D was more resistant to Zn and less resistant to Co than other TaMTP1-like members, and that TaMTP1-D was expressed at a higher level in the endosperm than other members. All results reveal that the use of TaMTP1-D for biofortification can substantially increase the content of Zn in the edible part of wheat and avoid the overaccumulation of Co, suggesting that TaMTP1-D is a potential Zn biofortifier / bioreinforcement.

36-year study reveals stability of a wild wheat population across microhabitats

Long-term genetic studies of wild populations are very scarce, but are essential for connecting ecological and population genetics models, and for understanding the dynamics of biodiversity. We present a study of a wild wheat population sampled over a 36-year period at high spatial resolution. We genotyped 832 individuals from regular sampling along transects during the course of the experiment. Genotypes were clustered into ecological microhabitats over scales of tens of metres, and this clustering was remarkably stable over the 36 generations of the study. Simulations show that it is difficult to determine whether this spatial and temporal stability reflects extremely limited dispersal or fine-scale local adaptation to ecological parameters. Using a common-garden experiment, we showed that the genotypes found in distinct microhabitats differ phenotypically. Our results provide a rare insight into the population genetics of a natural population over a long monitoring period.

Dosage effect genes modulate grain development in synthesized Triticum durum-Haynaldia villosa allohexaploid

Polyploidization in plants often leads to increased cell size and grain size, which may be affected by the increased genome dosage and transcription abundance. The synthesized Triticum durum (AABB)-Haynaldia villosa (VV) amphiploid (AABBVV) has significantly increased grain size, especially grain length, than the tetraploid and diploid parents. To investigate how polyploidization affects grain development at the transcriptional level, we perform transcriptome analysis using the immature seeds of T. durum, H. villosa, and the amphiploid. The dosage effect genes are contributed more by differentially expressed genes from genome V of H. villosa. The dosage effect genes overrepresent grain development-related genes. Interestingly, the vernalization gene TaVRN1 is among the positive dosage effect genes in the T. durum‒H. villosa and T. turgidum‒Ae. tauschii amphiploids. The expression levels of TaVRN1 homologs are positively correlated with the grain size and weight. The TaVRN1-B1 or TaVRN1-D1 mutation shows delayed florescence, decreased cell size, grain size, and grain yield. These data indicate that dosage effect genes could be one of the important explanations for increased grain size by regulating grain development. The identification and functional validation of dosage effect genes may facilitate the finding of valuable genes for improving wheat yield.

Tracing post-domestication historical events and screening pre-breeding germplasm from large gene pools in wheat in the absence of phenotype data

Wheat, particularly common wheat (Triticum aestivum L.), is a major crop accounting for 25% of the world cereal production and thriving in diverse ecogeographic regions. Its adaptation to diverse environments arises from its three distinct genomes adapted to different environments and post-domestication anthropogenic interventions. In search of key genomic regions revealing historic events and breeding significance to common wheat, we performed genome scan and genome-environment association (GEA) analyses using high-marker density genotype datasets. Whole-genome scans revealed highly differentiated regions on chromosomes 2A, 3B, and 4A. In-depth analyses corroborated our previous prediction of the 4A differentiated region signifying the separation between Spelt/Macha and other wheat types. Individual chromosome scans captured key introgressions, including one from T. timopheevii and one from Thinopyrum ponticum on 2B and 3D, respectively, as well as known genes such as Vrn-A1 on 5A. GEA highlighted loci linked to latitude-induced environmental variations, influencing traits such as photoperiodism and responses to abiotic stress. Variation at the Vrn-A1 locus on 5A assigned accessions to two haplotypes (6% and 94%). Further analysis on Vrn-A1 coding gene revealed four subgroups of the major haplotype, while the minor haplotype remained undifferentiated. Analyses at differentiated loci mostly dichotomized the population, illustrating the possibility of isolating pre-breeding materials with desirable traits from large gene pools in the absence of phenotype data. Given the current availability of broad genetic data, the genome-scan-GEA hybrid can be an efficient and cost-effective approach for pinpointing environmentally resilient pre-breeding germplasm from vast gene pools, including gene banks regardless of trait characterization.

The Impact of Ganoderma lucidum (Curtis) P. Karst. Supplementation on the Technological, Chemical, and Quality Parameters of Wheat Bread

This study explores the incorporation of Ganoderma lucidum (Curtis) P. Karst. (Reishi mushroom) into wheat bread to develop a functional food with enhanced nutritional value. Reishi powder was added to bread formulations at levels of 3%, 6%, 9%, and 12% to assess its effects on physicochemical, nutritional, and sensory properties. The 12% Reishi supplementation resulted in a twofold increase in total dietary fibre (from 7.21 g to 17.08 g per 100 g dry matter) and significant (p < 0.05) elevations in mineral content, particularly calcium (68%), iron (32%), and manganese (61.9%). Carbohydrate content decreased markedly by 27%, contributing to a 19.33% reduction in caloric value. Reishi addition improved bread yield and reduced baking losses, enhancing production efficiency. However, higher Reishi levels negatively impacted bread volume, possibly due to interference with gluten network formation. An increase in crumb moisture was observed, contributing to extended freshness. Sensory evaluation revealed that loaves of bread containing up to 6% Reishi were acceptable to consumers, whereas higher levels detrimentally affected flavour and aroma. Therefore, Reishi-enriched bread, particularly with 6% supplementation, presents a promising functional alternative to conventional wheat bread, optimising nutritional benefits while maintaining consumer acceptability.

Transcription factors and genome biases in polyploid crops

Nuclear protein transcription factors (TFs) regulate all biological processes in plants and are necessary for gene regulation. The transcription of genes during plant growth and development and their response to environmental cues are regulated by TF binding to specific promoter regions in the genomic DNA. Polyploid plants with several sets of chromosomes frequently display intricate genomic biases concerning TF expression. One or more subgenomes may dominate in terms of gene expression, leading to subgenome biases or dominance. These biases can influence various aspects of the crop's biology, including its growth, development, and adaptation. Advances in genomics have speed up the improvement of many important agricultural diploid crops, yet comparable endeavours in polyploid crops have been more challenging. This challenge primarily stems from the large size and intricate nature of the complex genome in polyploid crops, along with the need for comprehensive genome assembly data for such crop varieties as bread wheat, cotton and sugarcane. Several studies have evaluated the biased/asymmetric gene expression patterns, including TFs, within the polyploid crop genomes. In many polyploid crops, not all homologues of TF genes contribute equally to the phenotype. Here, we have examined polyploid crop plants for homeolog gene expression, emphasizing TFs. It is observed that the polyploids retain many gene alleles as functional homeologs that define important features involved in stress response, sugar metabolism, and fibre formation. The possible molecular mechanism describing the structural and epigenetic basis of differential subgenomic TF expression in polyploids is discussed.

Transcriptomic response to nitrogen availability reveals signatures of adaptive plasticity during tetraploid wheat domestication

The domestication of crops, coupled with agroecosystem development, is associated with major environmental changes and provides an ideal model of phenotypic plasticity. Here, we examined 32 genotypes of three tetraploid wheat (Triticum turgidum L.) subspecies, wild emmer, emmer, and durum wheat, which are representative of the key stages in the domestication of tetraploid wheat. We developed a pipeline that integrates RNA-Seq data and population genomics to assess gene expression plasticity and identify selection signatures under diverse nitrogen availability conditions. Our analysis revealed differing gene expression responses to nitrogen availability across primary (wild emmer to emmer) and secondary (emmer to durum wheat) domestication. Notably, nitrogen triggered the expression of twice as many genes in durum wheat compared to that in emmer and wild emmer. Unique selection signatures were identified at each stage: primary domestication mainly influenced genes related to biotic interactions, whereas secondary domestication affected genes related to amino acid metabolism, in particular lysine. Selection signatures were found in differentially expressed genes (DEGs), notably those associated with nitrogen metabolism, such as the gene encoding glutamate dehydrogenase (GDH). Overall, our study highlights the pivotal role of nitrogen availability in the domestication and adaptive responses of a major food crop, with varying effects across different traits and growth conditions.

Genome-wide identification of the E-class gene family in wheat: evolution, expression, and interaction

Introduction

Wheat (Triticum aestivum L.) is among themost important crop worldwide. Given a growing population and changing climate, enhancing wheat yield is of great importance. Yield is closely associated with flower and spike development, and E-class genes play important roles in the flower and kernel development of plants. Currently, the absence of systematic analysis on the E gene family hinders our comprehension of their roles in plant growth and development.

Methods

Identify E-class genes based on homologous sequence searches. Analyze the identified E-class genes through a series of gene family analyses. Determine the expression levels of wheat E-class genes by searching public databases. Validate the functions of these genes by transforming them into Arabidopsis. Finally, determine the interactions between the genes through yeast two-hybrid experiments.

Results

Fifteen E-class genes (TaEs) were identified in common wheat. Nine E-class genes were detected in five ancestral/closely related species, including one in Aegilops tauschii (AtE), one in T. Urartu (TuEs), two in T. turgidum (TtEs), two in T. dicoccoides (TdEs), and three in T. spelta (TsEs). The 24 E-class genes were classified into three subgroups using a phylogenetic approach. All genes were highly expressed in spikes, and most were only highly expressed at the floret meristem stage. The effects of TaSEP5-A on flowering and growth cycles were confirmed in homologous mutants and transgenic Arabidopsis thaliana. The E-class genes were able to regulate the growth cycle of Arabidopsis. Finally, we confirmed the interactions between TaSEP5-A and other wheat E-class genes based on yeast two-hybrid assays.

Discussion

Our findings provide information regarding the E-class genes in wheat and will potentially promote the application of these genes in wheat improvement.

Adaptation of Fusarium Head Blight Pathogens to Changes in Agricultural Practices and Human Migration

Fusarium head blight (FHB) is one of the most destructive wheat diseases worldwide. To understand the impact of human migration and changes in agricultural practices on crop pathogens, here population genomic analysis with 245 representative strains from a collection of 4,427 field isolates of Fusarium asiaticum, the causal agent of FHB in Southern China is conducted. Three populations with distinct evolution trajectories are identifies over the last 10,000 years that can be correlated with historically documented changes in agricultural practices due to human migration caused by the Southern Expeditions during the Jin Dynasty. The gradual decrease of 3ADON-producing isolates from north to south along with the population structure and spore dispersal patterns shows the long-distance (>250 km) dispersal of F. asiaticum. These insights into population dynamics and evolutionary history of FHB pathogens are corroborated by a genome-wide analysis with strains originating from Japan, South America, and the USA, confirming the adaptation of FHB pathogens to cropping systems and human migration.

Wild grass-derived alleles represent a genetic architecture for the resilience of modern common wheat to stresses

This review explores the integration of wild grass-derived alleles into modern bread wheat breeding to tackle the challenges of climate change and increasing food demand. With a focus on synthetic hexaploid wheat, this review highlights the potential of genetic variability in wheat wild relatives, particularly Aegilops tauschii, for improving resilience to multifactorial stresses like drought, heat, and salinity. The evolutionary journey of wheat (Triticum spp.) from diploid to hexaploid species is examined, revealing significant genetic contributions from wild grasses. We also emphasize the importance of understanding incomplete lineage sorting in the genomic evolution of wheat. Grasping this information is crucial as it can guide breeders in selecting the appropriate alleles from the gene pool of wild relatives to incorporate into modern wheat varieties. This approach improves the precision of phylogenetic relationships and increases the overall effectiveness of breeding strategies. This review also addresses the challenges in utilizing the wheat wild genetic resources, such as the linkage drag and cross-compatibility issues. Finally, we culminate the review with future perspectives, advocating for a combined approach of high-throughput phenotyping tools and advanced genomic techniques to comprehensively understand the genetic and regulatory architectures of wheat under stress conditions, paving the way for more precise and efficient breeding strategies.

Engineering the future cereal crops with big biological data: toward intelligence-driven breeding by design

How to feed 10 billion human populations is one of the challenges that need to be addressed in the following decades, especially under an unpredicted climate change. Crop breeding, initiating from the phenotype-based selection by local farmers and developing into current biotechnology-based breeding, has played a critical role in securing the global food supply. However, regarding the changing environment and ever-increasing human population, can we breed outstanding crop varieties fast enough to achieve high productivity, good quality, and widespread adaptability? This review outlines the recent achievements in understanding cereal crop breeding, including the current knowledge about crop agronomic traits, newly developed techniques, crop big biological data research, and the possibility of integrating them for intelligence-driven breeding by design, which ushers in a new era of crop breeding practice and shapes the novel architecture of future crops. This review focuses on the major cereal crops, including rice, maize, and wheat, to explain how intelligence-driven breeding by design is becoming a reality.

A neat wheat trick to hide genes from selection

A recent study by Li et al. demonstrated that the removal of like heterochromatin protein 1 (LHP1) in common wheat causes developmental drawbacks, yet confers resistance to stripe rust infection. Due to its role in regulating diversified defense genes, LHP1 was suggested to be an epigenetic gatekeeper potentially promoting adaptive evolution in allopolyploid wheat.

Epigenomic identification of vernalization cis-regulatory elements in winter wheat

BACKGROUND

Winter wheat undergoes vernalization, a process activated by prolonged exposure to low temperatures. During this phase, flowering signals are generated and transported to the apical meristems, stimulating the transition to the inflorescence meristem while inhibiting tiller bud elongation. Although some vernalization genes have been identified, the key cis-regulatory elements and precise mechanisms governing this process in wheat remain largely unknown.

RESULTS

In this study, we construct extensive epigenomic and transcriptomic profiling across multiple tissues-leaf, axillary bud, and shoot apex-during the vernalization of winter wheat. Epigenetic modifications play a crucial role in eliciting tissue-specific responses and sub-genome-divergent expressions during vernalization. Notably, we observe that H3K27me3 primarily regulates vernalization-induced genes and has limited influence on vernalization-repressed genes. The integration of these datasets enables the identification of 10,600 putative vernalization-related regulatory elements including distal accessible chromatin regions (ACRs) situated 30Kb upstream of VRN3, contributing to the construction of a comprehensive regulatory network. Furthermore, we discover that TaSPL7/15, integral components of the aging-related flowering pathway, interact with the VRN1 promoter and VRN3 distal regulatory elements. These interactions finely regulate their expressions, consequently impacting the vernalization process and flowering.

CONCLUSIONS

Our study offers critical insights into wheat vernalization's epigenomic dynamics and identifies the putative regulatory elements crucial for developing wheat germplasm with varied vernalization characteristics. It also establishes a vernalization-related transcriptional network, and uncovers that TaSPL7/15 from the aging pathway participates in vernalization by directly binding to the VRN1 promoter and VRN3 distal regulatory elements.

Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants

Premise

The genomes of polyploid plants archive the evolutionary events leading to their present forms. However, plant polyploid genomes present numerous hurdles to the genome comparison algorithms for classification of polyploid types and exploring genome dynamics.

Methods

Here, the problem of intra- and inter-genome comparison for examining polyploid genomes is reframed as a metagenomic problem, enabling the use of the rapid and scalable MinHashing approach. To determine how types of polyploidy are described by this metagenomic approach, plant genomes were examined from across the polyploid spectrum for both k-mer composition and frequency with a range of k-mer sizes. In this approach, no subgenome-specific k-mers are identified; rather, whole-chromosome k-mer subspaces were utilized.

Results

Given chromosome-scale genome assemblies with sufficient subgenome-specific repetitive element content, literature-verified subgenomic and genomic evolutionary relationships were revealed, including distinguishing auto- from allopolyploidy and putative progenitor genome assignment. The sequences responsible were the rapidly evolving landscape of transposable elements. An investigation into the MinHashing parameters revealed that the downsampled k-mer space (genomic signatures) produced excellent approximations of sequence similarity. Furthermore, the clustering approach used for comparison of the genomic signatures is scrutinized to ensure applicability of the metagenomics-based method.

Discussion

The easily implementable and highly computationally efficient MinHashing-based sequence comparison strategy enables comparative subgenomics and genomics for large and complex polyploid plant genomes. Such comparisons provide evidence for polyploidy-type subgenomic assignments. In cases where subgenome-specific repeat signal may not be adequate given a chromosomes' global k-mer profile, alternative methods that are more specific but more computationally complex outperform this approach.

Genotype-by-environment interaction and stability analysis of grain yield of bread wheat (Triticum aestivum L.) genotypes using AMMI and GGE biplot analyses

Bread wheat is a vital staple crop worldwide; including in Ethiopia, but its production is prone to various environmental constraints and yield reduction associated with adaptation. To identify adaptable genotypes, a total of 12 bread wheat genotypes (G1 to G12) were evaluated for their genotype-environment interaction (GEI) and stability across three different environments for two years using Additive Main Effect and Multiplicative Interaction (AMMI) and genotype main effect plus genotype-by-environment interaction (GGE) biplots analysis. GEI is a common phenomenon in crop improvement and is of significant importance in genotype assessment and recommendation. According to combined analysis of variance, grain yield was considerably impacted by environments, genotypes, and GEI. AMMI and GGE biplots analysis also provided insights into the performance and stability of the genotypes across diverse environmental conditions. Among the 12 genotypes, G6 was selected by AMMI biplot analysis as adaptive and high-yielding genotype; G5 and G7 demonstrated high stability and minimal interaction with the environment, as evidenced by their IPCA1 values. G7 was identified as the most stable and high-yielding genotype. The GGE biplot's polygon view revealed that the highest grain yield was obtained from G6 in environment three (E3). E3 was selected as the ideal environment by the GGE biplot. The top three stable genotypes identified by AMMI stability value (ASV) were G5, G7, and G10, while the most stable genotype determined by Genotype Selection Index (GSI) was G7. Even though G6 was a high yielder, it was found to be unstable according to ASV and ranked third in stability according to GSI. Based on the study's findings, the GGE biplot genotype view for grain yield identified Tay genotype (G6) to be the most ideal genotype due to its high grain yield and stability in diverse environments. G7 showed similar characteristics and was also stable. These findings provide valuable insights to breeders and researchers for selecting high-yielding and stable, as well as high-yielding specifically adapted genotypes.

Spontaneous chromosome instability and tissue culture-induced karyotypic alteration in wheat-Thinopyrum intermedium alien addition lines

MAIN CONCLUSION

Wheat lines harboring wild-relative chromosomes can be karyotypically unstable during long-term maintenance. Tissue culture exacerbates chromosomal instability but appears inefficient to induce somatic homoeologous exchange between alien and wheat chromosomes. We assessed if long-term refrigerator storage with regular renewal via self-fertilization, a widely used practice for crop germplasm maintenance, would ensure genetic fidelity of alien addition lines, and explored the possibility of inducing somatic homoeologues exchange by tissue culture. We cytogenetically characterized sampled stock seeds of originally confirmed 12 distinct wheat-Thinopyrum intermedium alien addition lines (dubbed TAI lines), and subjected immature embryos of the TAI lines to tissue culture. We find eight of the 12 TAI lines were karyotypically departed from their original identity as bona fide disomic alien addition lines due to extensive loss of whole-chromosomes of both Th. intermedium and wheat origins during the ca. 3-decade storage. Rampant numerical chromosome variations (NCVs) involving both alien and wheat chromosomes were detected in regenerated plants of all 12 studied TAI lines, but at variable rates among the wheat sub-genomes and chromosomes. Compared with NCVs, structural chromosome variations (SCVs) occurred at substantially lower rates, and no SCV involving the added alien chromosomes was observed. The NCVs manifested only moderate effects on phenotypes of the regenerated plants under field conditions.

Telomere-to-telomere reference genome for Panax ginseng highlights the evolution of saponin biosynthesis

Ginseng (Panax ginseng) is a representative of Chinese traditional medicine, also used worldwide, while the triterpene saponin ginsenoside is the most important effective compound within it. Ginseng is an allotetraploid, with complex genetic background, making the study of its metabolic evolution challenging. In this study, we assembled a telomere-to-telomere ginseng reference genome, constructed of 3.45 Gb with 24 chromosomes and 77 266 protein-coding genes. Additionally, the reference genome was divided into two subgenomes, designated as subgenome A and B. Subgenome A contains a larger number of genes, whereas subgenome B has a general expression advantage, suggesting that ginseng subgenomes experienced asymmetric gene loss with biased gene expression. The two subgenomes separated approximately 6.07 million years ago, and subgenome B shows the closest relation to Panax vietnamensis var. fuscidiscus. Comparative genomics revealed an expansion of gene families associated with ginsenoside biosynthesis in both ginseng subgenomes. Furthermore, both tandem duplications and proximal duplications play crucial roles in ginsenoside biosynthesis. We also screened functional genes identified in previous research and found that some of these genes located in colinear regions between subgenomes have divergence functions, revealing an unbalanced evolution in both subgenomes and the saponin biosynthesis pathway in ginseng. Our work provides important resources for future genetic studies and breeding programs of ginseng, as well as the biosynthesis of ginsenosides.

Comprehensive genome-wide analysis of wheat xylanase inhibitor protein (XIP) genes: unveiling their role in Fusarium head blight resistance and plant immune mechanisms

In this comprehensive genome-wide study, we identified and classified 83 Xylanase Inhibitor Protein (XIP) genes in wheat, grouped into five distinct categories, to enhance understanding of wheat's resistance to Fusarium head blight (FHB), a significant fungal threat to global wheat production. Our analysis reveals the unique distribution of XIP genes across wheat chromosomes, particularly at terminal regions, suggesting their role in the evolutionary expansion of the gene family. Several XIP genes lack signal peptides, indicating potential alternative secretion pathways that could be pivotal in plant defense against FHB. The study also uncovers the sequence homology between XIPs and chitinases, hinting at a functional diversification within the XIP gene family. Additionally, the research explores the association of XIP genes with plant immune mechanisms, particularly their linkage with plant hormone signaling pathways like abscisic acid and jasmonic acid. XIP-7A3, in particular, demonstrates a significant increase in expression upon FHB infection, highlighting its potential as a key candidate gene for enhancing wheat's resistance to this disease. This research not only enriches our understanding of the XIP gene family in wheat but also provides a foundation for future investigations into their role in developing FHB-resistant wheat cultivars. The findings offer significant implications for wheat genomics and breeding, contributing to the development of more resilient crops against fungal diseases.

Genomic insights into the origin and evolution of spelt (Triticum spelta L.) as a valuable gene pool for modern wheat breeding

Spelt (Triticum aestivum ssp. spelta) is an important wheat subspecies mainly cultivated in Europe before the 20th century that has contributed to modern wheat breeding as a valuable genetic resource. However, relatively little is known about the origins and maintenance of spelt populations. Here, using resequencing data from 416 worldwide wheat accessions, including representative spelt wheat, we demonstrate that European spelt emerged when primitive hexaploid wheat spread to the west and hybridized with pre-settled domesticated emmer, the putative maternal donor. Genomic introgression regions from domesticated emmer confer spelt's primitive morphological characters used for species taxonomy, such as tenacious glumes and later flowering. We propose a haplotype-based "spelt index" to identify spelt-type wheat varieties and to quantify utilization of the spelt gene pool in modern wheat cultivars. This study reveals the genetic basis for the establishment of the spelt wheat subspecies in a specific ecological niche and the vital role of the spelt gene pool as a unique germplasm resource in modern wheat breeding.

Are cereal grasses a single genetic system?

In 1993, a passionate and provocative call to arms urged cereal researchers to consider the taxon they study as a single genetic system and collaborate with each other. Since then, that group of scientists has seen their discipline blossom. In an attempt to understand what unity of genetic systems means and how the notion was borne out by later research, we survey the progress and prospects of cereal genomics: sequence assemblies, population-scale sequencing, resistance gene cloning and domestication genetics. Gene order may not be as extraordinarily well conserved in the grasses as once thought. Still, several recurring themes have emerged. The same ancestral molecular pathways defining plant architecture have been co-opted in the evolution of different cereal crops. Such genetic convergence as much as cross-fertilization of ideas between cereal geneticists has led to a rich harvest of genes that, it is hoped, will lead to improved varieties.

Exploring the patterns of evolution: Core thoughts and focus on the saltational model

The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.